There's a button at the bottom of every puzzle, that lets you save your progress and come back to the puzzle later. Clicking it doesn't seem to pause the timer though (on Firefox?) -- so if you come back four hours later, your time when you re-open the puzzle is over four hours long.

It calculates the 4+ hour solution time into your totals for that puzzle type, too, under "My Scores". This severely throws off averages.

If you choose not to finish the puzzle at all, that starts lowering your completion percentage.

I'm not sure what that button is supposed to be for, or what a player is supposed to do if they need to leave the game suddenly in the middle of a puzzle. Do they just take the hit to completion percentage? Or the hit to completion time?

It seems like there could be a cutoff point, past which times aren't counted into the total for that puzzle type. For the smaller puzzles, anything over 1800 seconds (30 minutes) is probably worth not counting into the statistics -- for both an individual user, and for that individual puzzle. It skews the average significantly, and makes it Much easier to end up in the top few percent for everyone thereafter.

For bigger puzzles... I've ended up leaving a puzzle and coming back 5+ hours later once or twice. 20K seconds is more than anyone really needs....